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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattatcgatccgcatctaatttactactaagttcagcgtctagctatgtttgtactcagtgttgagatgtcagcactaatcagttgtctaatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTGAATGAGGAAATTTTACGCCTCGAACGAGAGGAGAGTGACGATAATAGTC

Basic information

species Physcomitrella patens
transcript PP1S222_130V6.3
intron # 4
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|162200922|gb|FC377325.1|FC377325
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|67570167|gb|BJ942991.1|BJ942991
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|162181666|gb|FC358696.1|FC358696
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|100443300|gb|BY963596.1|BY963596
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|18362678|gb|BJ194749.1|BJ194749
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|67574627|gb|BJ947451.1|BJ947451
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|18372863|gb|BJ204465.1|BJ204465
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGG
EST: gi|162170244|gb|FC347364.1|FC347364
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|18374599|gb|BJ206177.1|BJ206177
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|162220370|gb|FC395738.1|FC395738
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|18363986|gb|BJ196059.1|BJ196059
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAA
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAA
EST: gi|162196667|gb|FC374632.1|FC374632
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|18347979|gb|BJ180026.1|BJ180026
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|18365214|gb|BJ197288.1|BJ197288
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|162257683|gb|FC433610.1|FC433610
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|18373428|gb|BJ205006.1|BJ205006
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAG
EST: gi|162168431|gb|FC344407.1|FC344407
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|18359898|gb|BJ191959.1|BJ191959
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGG
EST: gi|18374996|gb|BJ206574.1|BJ206574
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|18360287|gb|BJ192349.1|BJ192349
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|100434971|gb|BY960896.1|BY960896
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|162149665|gb|FC326716.1|FC326716
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|18355255|gb|BJ187314.1|BJ187314
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
EST: gi|162162513|gb|FC338607.1|FC338607
EST:     CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG                         ATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG
genomic: CAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAGgtacgcgaca ... aatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtttgtactcagtgttgagatgtcagcactaatcagttgtctaatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTGAATGAGGAAATTTTACGCCTCGAACGAGAGGAGAGTGACGATAATAGTC
                                          tctaattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattatcgatccgcatctaatttactactaagttcagcgtctagctatgtttgtactcagtgttgagatgtcagcactaatcagttgtctaatttggtagATTACATACATACACGGGGCGTATGATGCTGATGAAGGTTTTATCAAGTTGAATGAGGAAATTTTACGCCTCGAACGAGAGGAGAGTGACGATAATAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA